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Downloads and Upgrades Jul 1, 2011

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Strand Scientific Intelligence and Biobase have combined their respective products: Avadis NGS and Genome Trax.

By purchasing the integrated version of Genome Trax from Strand, Avadis NGS users will have access to Biobase's Transfac, which contains more than 3,000 regulatory sites; HGMD Professional, which includes 80,000 disease-linked mutations; over 600,000 ChIP-seq fragments; post-translational modifications; and transcription start sites.

In addition, license holders are given access to the Genome Trax online database, which holds additional information, including complete source citations.


Elsevier has added two new applications from Molecular Connections, a life science informatics company, to SciVerse Applications beta.

The first, Ask Extractor is based on Molecular Connections' XTractor, a platform for discovery, analysis, and modeling of biomedical information. The application provides search suggestions for life sciences terms entered into SciVerse Hub and SciVerse ScienceDirect. The second application, Journal Trends, enables users to discover top journals as a result of a given search query.


GenePattern 3.3.2 is now available.

This release includes the ability to upload files larger than 2 gigabytes, improved handling and visualization of uploaded files, and automatic launching and viewing of large data files with the Integrative Genomics Viewer.

Version 3.3.2 can be downloaded here and is also available for use on the GenePattern public server.


Gene Codes has released Sequencher 5.0.

The release incorporates new DNA sequence data alignment algorithms, such as Clustal, Maq, GSNAP, and Tablet, with SNP and methylation analysis for next-generation DNA sequence data analysis.


The Swiss Institute of Bioinformatics has launched an updated version of its web portal ExPASy, which provides a point of entry to more than 120 SIB bioinformatics resources in different areas including proteomics, genomics, phylogeny, systems biology, evolution, population genetics, and transcriptomics.

Among its capabilities is a new search feature that lets users query databases for content, and a visual guidance interface that lets users discover resources based on visual aids such as graphical images and tag clouds.


The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.